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Optimal alignments in linear space
Abstract
Space, not time, is often the limiting factor when computing optimal sequence alignments, and a number of recent papers in the biology literature have proposed space-saving strategies. However, a 1975 computer science paper by Hirschberg presented a method that is superior to the new proposals, both in theory and in practice. The goal of this paper is to give Hirschberg's idea the visibility it deserves by developing a linear-space version of Gotoh's algorithm, which accommodates affine gap penalties. A portable C-software package implementing this algorithm is available on the BIONET free of charge.
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Citations
Cited by
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
Altschul, S. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.17.3389 · Cited by 73,302
Thompson, J. D., Higgins, D. G., & Gibson, T. J. (1994) · Nucleic Acids Research · doi:10.1093/nar/22.22.4673 · Cited by 64,617
VSEARCH: a versatile open source tool for metagenomics
(2016) · doi:10.7717/peerj.2584 · Cited by 10,773
CAP3: A DNA Sequence Assembly Program
Huang, X., & Madan, A. (1999) · Genome Research · doi:10.1101/gr.9.9.868 · Cited by 5,261
Multiple sequence alignment with the Clustal series of programs
Chenna, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg500 · Cited by 4,875
Metadata
- Authors
- Myers, E. W., & Miller, W.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 1988
- Volume
- 4
- Issue
- 1
- Pages
- 11-17
- ISSN
- 0266-7061 (ISSN-L)
- 1367-4803
- 1460-2059
- OpenAlex
- W2108215151
- Cited by
- 1,235
- References
- 0
- FWCI
- 18.22
- Type
- journal article
- Language
- en
- Open access
- closed
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- CoChat. (2026). Citation check: Optimal alignments in linear space. https://app.cochat.ai/papers/10.1093/bioinformatics/4.1.11
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- Myers, E. W., & Miller, W. (1988). Optimal alignments in linear space. Bioinformatics. https://doi.org/10.1093/bioinformatics/4.1.11
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